Disbled B2, Salmon and Hapmap indexing

src/CroCo_v1.1.sh

@@ -58,11 +58,11 @@ if [ $RECAT == "no" ]; then
 ### index contigs for the selected tool
  case "$TOOL" in
   B) toolidx="ALL_transcripts_bowtie_index"; if [ ! -d $out/$toolidx ]; then mkdir $out/$toolidx; bowtie-build --offrate 3 $out/ALL_transcripts.fasta $out/$toolidx/$toolidx ;fi ;;
-  B2) toolidx="ALL_transcripts_bowtie2_index"; if [ ! -d $out/$toolidx ]; then mkdir $out/$toolidx; bowtie2-build --offrate 3 $out/ALL_transcripts.fasta $out/$toolidx/$toolidx ;fi ;;
+  #B2) toolidx="ALL_transcripts_bowtie2_index"; if [ ! -d $out/$toolidx ]; then mkdir $out/$toolidx; bowtie2-build --offrate 3 $out/ALL_transcripts.fasta $out/$toolidx/$toolidx ;fi ;;
   K) toolidx="ALL_transcripts_kallisto_index"; if [ ! -f $out/$toolidx ]; then kallisto index -i $out/$toolidx $out/ALL_transcripts.fasta; fi ;;
-  S) toolidx="ALL_transcripts_salmon_index" ; if [ ! -d $out/$toolidx ]; then salmon --no-version-check index -t $out/ALL_transcripts.fasta -i $out/$toolidx; fi ;;
+  #S) toolidx="ALL_transcripts_salmon_index" ; if [ ! -d $out/$toolidx ]; then salmon --no-version-check index -t $out/ALL_transcripts.fasta -i $out/$toolidx; fi ;;
   R) toolidx="ALL_transcripts_rapmap_index" ; if [ ! -d $out/$toolidx ]; then rapmap quasiindex -t $out/ALL_transcripts.fasta -p -x $PROCESSORS -i $out/$toolidx; fi ;;
-  H) toolidx="ALL_transcripts_hpg_index" ; if [ ! -d $out/$toolidx ]; then mkdir $out/$toolidx; hpg-aligner build-sa-index -g $out/ALL_transcripts.fasta -i $out/$toolidx; fi ;;
+  #H) toolidx="ALL_transcripts_hpg_index" ; if [ ! -d $out/$toolidx ]; then mkdir $out/$toolidx; hpg-aligner build-sa-index -g $out/ALL_transcripts.fasta -i $out/$toolidx; fi ;;
  esac
  echo -e "\nIndex built : $out/$toolidx\n"
 

src/calc_edgeR_TMM.R

-
-#Rscript --vanilla calc_edgeR_TMM.R file.txt
-
-calcFactorWeighted <- function (obs, ref, libsize.obs = NULL, libsize.ref = NULL, logratioTrim = 0.3,
-    sumTrim = 0.05, doWeighting = TRUE, Acutoff = -1e+10)
-{
-    if (all(obs == ref))
-        return(1)
-    obs <- as.numeric(obs)
-    ref <- as.numeric(ref)
-    if (is.null(libsize.obs))
-        nO <- sum(obs)
-    else nO <- libsize.obs
-    if (is.null(libsize.ref))
-        nR <- sum(ref)
-    else nR <- libsize.ref
-    logR <- log2((obs/nO)/(ref/nR))
-    absE <- (log2(obs/nO) + log2(ref/nR))/2
-    v <- (nO - obs)/nO/obs + (nR - ref)/nR/ref
-    fin <- is.finite(logR) & is.finite(absE) & (absE > Acutoff)
-    logR <- logR[fin]
-    absE <- absE[fin]
-    v <- v[fin]
-    n <- sum(fin)
-    loL <- floor(n * logratioTrim) + 1
-    hiL <- n + 1 - loL
-    loS <- floor(n * sumTrim) + 1
-    hiS <- n + 1 - loS
-    keep <- (rank(logR) >= loL & rank(logR) <= hiL) & (rank(absE) >=
-        loS & rank(absE) <= hiS)
-    if (doWeighting)
-        2^(sum(logR[keep]/v[keep], na.rm = TRUE)/sum(1/v[keep],
-            na.rm = TRUE))
-    else 2^(mean(logR[keep], na.rm = TRUE))
-}
-
-calcFactorQuantile <- function (data, lib.size, p = 0.75)
-{
-    y <- t(t(data)/lib.size)
-    f <- apply(y, 2, function(x) quantile(x, p = p))
-}
-
-calcNormFactors <- function (object, method = c("TMM", "RLE", "upperquartile", "none"),
-    refColumn = NULL, logratioTrim = 0.3, sumTrim = 0.05, doWeighting = TRUE,
-    Acutoff = -1e+10, p = 0.75)
-{
-    if (is(object, "DGEList")) {
-        x <- as.matrix(object$counts)
-        lib.size <- object$samples$lib.size
-    }
-    else {
-        x <- as.matrix(object)
-        lib.size <- colSums(x)
-    }
-    method <- match.arg(method)
-    allzero <- rowSums(x > 0) == 0
-    if (any(allzero))
-        x <- x[!allzero, , drop = FALSE]
-    if (nrow(x) == 0 || ncol(x) == 1)
-        method = "none"
-    f <- switch(method, TMM = {
-        f75 <- calcFactorQuantile(data = x, lib.size = lib.size,
-            p = 0.75)
-        if (is.null(refColumn)) refColumn <- which.min(abs(f75 -
-            mean(f75)))
-        if (length(refColumn) == 0 | refColumn < 1 | refColumn >
-            ncol(x)) refColumn <- 1
-        f <- rep(NA, ncol(x))
-        for (i in 1:ncol(x)) f[i] <- calcFactorWeighted(obs = x[,
-            i], ref = x[, refColumn], libsize.obs = lib.size[i],
-            libsize.ref = lib.size[refColumn], logratioTrim = logratioTrim,
-            sumTrim = sumTrim, doWeighting = doWeighting, Acutoff = Acutoff)
-        f
-    }, RLE = calcFactorRLE(x)/lib.size, upperquartile = calcFactorQuantile(x,
-        lib.size, p = p), none = rep(1, ncol(x)))
-    f <- f/exp(mean(log(f)))
-    if (is(object, "DGEList")) {
-        object$samples$norm.factors <- f
-        return(object)
-    }
-    else {
-        return(f)
-    }
-}
-
-args = commandArgs(trailingOnly=TRUE)
-z = read.table(args[2],sep=",",header=T)
-calcNormFactors(z)